1. M. Vidal, Interactome modeling, FEBS Lett. 579, 1834–1838 (2005).
2. G.T. Hart, A.K. Ramani, E.M. Marcotte, How complete are current yeast and human protein interaction networks? Gen. Biol. 7(11), 120 (2006).
3. C. von Mering et al., Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417, 399–401 (2002).
4. M.E. Cusick, et al., Literature-curated protein interaction datasets, Nat. Meth. 6, 39–46 (2009), doi:10.1038/nmeth.1284.
5. S. Brohee, J. van Helden, Evaluation of clustering algorithms for protein–protein interaction networks, BMC Bioinform. 7(488), 1–19 (2006).
6. S. Fortunato, M. Barthelemy, Resolution limit in community detection. PNAS 104, 36–41 (2007).
7. M. Roswall, C.T. Bergstrom, An information-theoretic framework for resolving community structure in complex networks. PNAS 104(18), 7327–7331 (2007).
8. A. Clauset, C.R. Shalizi, M.E.J. Newman, Power–law distributions in empirical data. SIAM Rev. 51(4), 661–703 (2009).
9. L.dF. Costa, F.A. Rodrigues, G. Travieso, P.R. Villas Boas, Characterization of complex networks: a survey of measurements. Adv. Phys. 56, 167–242 (2007).
10. P. Durek, D. Walther, The integrated analysis of metabolic and protein interaction networks reveals novel molecular organization principles. BMC Syst. Biol. 2, 100 (2008).
11. C. Huthmacher, C. Gille, H.G. Holzhütter, A computational analysis of protein interactions in metabolic networks reveals novel enzyme pairs potentially involved in metabolic channeling. J. Theor. Biol. 252(3), 456–464 (2008).
12. C. Huthmacher, C. Gille, H.G. Holzhütter, Computational analysis of protein–protein interactions in metabolic networks of E. coli and yeast. Genome Inform. 18, 162–172 (2007).
13. T. Reguly, et al., Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae, J. Biol. 5, 11 (2006).
14. U. de Lichtenberg, L.J. Jensen, S. Brunak, P. Bork, Dynamic complex formation during the yeast cell cycle, Science 307, 724–727 (2005).
15. http://mips.helmholtz-muenchen.de/genre/proj/yeast/
16. http://www.yeastgenome.org/
17. I.A. Maraziotis, K. Dimitrakopoulou, A. Bezerianos, An in silico method for detecting overlapping functional modules from composite biological networks. BMC Syst. Biol. 2(93), (2008), doi:10.1186/1752-0509-2-93.
18. Z. Dezso, Z.N. Oltvai, A.L. Barabasi, Bioinformatics analysis of experimentally determined protein complexes in the yeast Saccharomyces cerevisiae. Gen. Res. 13, 2450–2454 (2003).
19. J.F. Rual, et al., Towards a proteome-scale map of the human protein–protein interaction network. Nature 437, 1173–1178 (2005).
20. P.V. Missiuro, et al., Information flow analysis of interactome networks. PLos Computat. Biol. 5(4), e1000350 (2009).
21. A.C. Gavin, Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631–636 (2006).
22. A. Clauset, Finding local community structure in networks. Phys. Rev. E 72, 026132 (2005).
23. M.E.J. Newman, M. Girvan, Finding and evaluating community structure in networks. Phys. Rev. E 69, 026113 (2004).
24. G.D. Bader, W.V. Hogue, An automated method for finding molecular complexes in large protein interaction networks, BMC Bioinform. 4(2), 1–27 (2003).
25. D.O. Morgan, Regulation of the APC and the exit from mitosis. Nat. Cell Biol. 1, E47–E53 (1999), doi:10.1038/10039.
26. S. Jaspersen, et al., Cdc28/Cdk1 regulates spindle pole body duplication through phosphorylation of Spc42 and Mps1. Develop. Cell 7(2), 263–274 (2004).
27. G. Alexandru, et al., Phosphorylation of the cohesin subunit Scc1 by Polo/Cdc5 kinase regulates sister chromatid separation in yeast, Cell 105(4), 459–472 (2001).
28. B. Wilson, et al., The RSC chromatin remodeling complex bears an essential fungal-specific protein module with broad functional roles. Genetics 172, 795–809 (2006).
29. S. Uzawa, Spindle pole body duplication in fission yeast occurs at the G1/S boundary but maturation is blocked until exit from S by an event downstream of Cdc10+. MBoC 15(12), 5219–5230 (2004).
30. L. Vardy, T. Toda, The fission yeast gamma-tubulin complex is required in G(1) phase and is a component of the spindle assembly checkpoint. EMBO J. 19(22), 6098–6111 (2000).
31. E. Marras, E. Travaglione, E. Capobianco, Sub-modular resolution analysis by network mixture models. Statist. Appl. Genet. Mol. Biol. 9(1), 19 (2010).
32. M. Dehmer, A. Mowshowitz, A history of graph entropy measures. Inform. Sci. 181, 57–78 (2011).
33. A.L. Barabasi, R. Albert, Emergence of scaling in random networks, Science 286, 509–512 (1999).
34. R.J. Cho, et al., A genome-wide transcriptional analysis of the mitotic cell cycle, Mol. Cell 2, 65–73 (1998).
35. J.D. Han, et al., Evidence for dynamically organized modularity in the yeast protein–protein interaction network. Nature 430, 88–93 (2004).
36. P.T. Spellman, et al., Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization, Mol. Biol. Cell, 9(12), 3273–3297 (1998).